This module is a OpenCMISS(cm) buffer module to OpenCMISS(cellml). More...

Data Types
interface	cellml_create_cellml_to_field_map

interface	cellml_create_field_to_cellml_map

interface	cellml_field_component_get

interface	cellml_model_import

interface	cellml_variable_set_as_known

interface	cellml_variable_set_as_wanted

interface	map_cellml_field_type_to_variable_type
	Map a CellML field type to a CellML variable type from OpenCMISS(cellml). More...

interface	map_cellml_variable_type_to_field_type
	Map a CellML variable type from OpenCMISS(cellml) to a CellML field type. More...

Functions/Subroutines
subroutine, public	cellml_cellml_to_field_update (CELLML, ERR, ERROR,)
	Updates any mapped fields from the cellml fields. More...

subroutine, public	cellml_create_start (CELLML_USER_NUMBER, REGION, CELLML, ERR, ERROR,)
	Set up the CellML environment in the given region. For a given region, create a CellML environment that will be used to define CellML models in openCMISS. This will simply create and initialise an empty CellML environment object in the specified region with the specified unique identifier number. Also set some flag to indicate the CellML environment object is in the process of being created and should not yet be used. More...

subroutine, public	cellml_create_finish (CELLML, ERR, ERROR,)
	Finish creating the CellML environment. At this point we know all the variables that are known and wanted so can generate the final code. Check the provided CellML environment object and if it all looks good clear the "in progress" flag to indicate the object is now ready for use. More...

subroutine, public	cellml_destroy (CELLML, ERR, ERROR,)
	Destroys the given CellML environment. More...

subroutine, public	cellml_field_to_cellml_update (CELLML, ERR, ERROR,)
	Updates any cellml fields from the mapped fields. More...

subroutine	cellml_finalise (CELLML, ERR, ERROR,)
	Finalise a CellML environment and deallocate all memory. More...

subroutine	cellml_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment and deallocate all memory. More...

subroutine, public	cellml_field_maps_create_finish (CELLML, ERR, ERROR,)
	Finish creating the field maps for a CellML environment. More...

subroutine, public	cellml_field_maps_create_start (CELLML, ERR, ERROR,)
	Start the creation of field maps for a CellML environment. More...

subroutine	cellml_field_maps_finalise (CELLML_FIELD_MAPS, ERR, ERROR,)
	Finalise a CellML maps and deallocate all memory. More...

subroutine	cellml_field_maps_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML field mpas. More...

subroutine	cellml_model_finalise (CELLML_MODEL, ERR, ERROR,)
	Finalise a CellML model and deallocate all memory. More...

subroutine	cellml_model_initialise (CELLML_MODEL, ERR, ERROR,)
	Initialise a CellML model. More...

subroutine	cellml_model_map_finalise (CELLML_MODEL_MAP, ERR, ERROR,)
	Finalise a CellML model map and deallocate all memory. More...

subroutine	cellml_model_map_initialise (CELLML_MODEL_MAP, ERR, ERROR,)
	Initialise a CellML model map. More...

subroutine	cellml_model_maps_finalise (CELLML_MODEL_MAPS, ERR, ERROR,)
	Finalise a CellML model maps and deallocate all memory. More...

subroutine	cellml_model_maps_initialise (CELLML_MODEL_MAPS, ERR, ERROR,)
	Initialise a CellML model maps. More...

subroutine	cellml_model_import_c (CELLML, URI, MODEL_INDEX, ERR, ERROR,)
	Import the specified CellML model into the given CellML environment object. More...

subroutine	cellml_model_import_vs (CELLML, URI, MODEL_INDEX, ERR, ERROR,)
	Import the specified CellML model into the given CellML environment object. More...

subroutine	cellml_variable_set_as_known_c (CELLML, MODEL_INDEX, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be known - i.e., the variable's value will be set by an OpenCMISS field. More...

subroutine	cellml_variable_set_as_known_vs (CELLML, MODEL_USER_NUMBER, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be known - i.e., the variable's value will be set by an OpenCMISS field. More...

subroutine	cellml_variable_set_as_wanted_c (CELLML, MODEL_INDEX, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be wanted - i.e., the variable's value will used by an OpenCMISS field. More...

subroutine	cellml_variable_set_as_wanted_vs (CELLML, MODEL_USER_NUMBER, VARIABLE_ID, ERR, ERROR,)
	Sets a CellML model variable to be wanted - i.e., the variable's value will be used by an OpenCMISS field. More...

subroutine	cellml_create_cellml_to_field_map_c (CELLML, MODEL_INDEX, VARIABLE_ID, CELLML_PARAMETER_SET, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, ERR, ERROR,)
	Create a CellML model variable to field variable component map. More...

subroutine	cellml_create_cellml_to_field_map_vs (CELLML, MODEL_USER_NUMBER, VARIABLE_ID, CELLML_PARAMETER_SET, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, ERR, ERROR,)
	Create a CellML model variable to field variable component map. More...

subroutine	cellml_create_field_to_cellml_map_c (CELLML, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, MODEL_INDEX, VARIABLE_ID, CELLML_PARAMETER_SET, ERR, ERROR,)
	Create a field variable component to CellML model variable map. More...

subroutine	cellml_create_field_to_cellml_map_vs (CELLML, FIELD, VARIABLE_TYPE, COMPONENT_NUMBER, FIELD_PARAMETER_SET, MODEL_USER_NUMBER, VARIABLE_ID, CELLML_PARAMETER_SET, ERR, ERROR,)
	Create a field variable component to CellML model variable map. More...

subroutine, public	cellml_fieldmodeldofset (modelVariable, modelDofIdx, field, variableType, parameterSetIdx, componentIdx, value, err, error,)
	Set the dof in a field specified by a model DOF and component to a value. More...

subroutine	cellml_models_field_check (MODELS_FIELD, ERR, ERROR,)
	Checks a CellML environment models field for correctness. More...

subroutine, public	cellml_models_field_create_start (MODEL_FIELD_USER_NUMBER, CELLML, MODELS_FIELD, ERR, ERROR,)
	Start the creation of the models field for the given CellML environment. More...

subroutine, public	cellml_models_field_create_finish (CELLML, ERR, ERROR,)
	Finish the creation of the models field for the given CellML environment. More...

subroutine	cellml_models_field_finalise (MODELS_FIELD, ERR, ERROR,)
	Finalise a CellML environment models field and deallocate all memory. More...

subroutine, public	cellml_models_field_get (CELLML, MODELS_FIELD, ERR, ERROR,)
	Returns the models field for the given CellML environment. More...

subroutine	cellml_models_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment models field. More...

subroutine, public	cellml_state_field_create_start (STATE_FIELD_USER_NUMBER, CELLML, STATE_FIELD, ERR, ERROR,)
	Start the creation of the state field for the given CellML environment. More...

subroutine, public	cellml_state_field_create_finish (CELLML, ERR, ERROR,)
	Finialse the creation of the state field for the given CellML environment. Finish creating the state variable field for the provided CellML environment. More...

subroutine	cellml_state_field_finalise (STATE_FIELD, ERR, ERROR,)
	Finalise a CellML environment state field and deallocate all memory. More...

subroutine, public	cellml_state_field_get (CELLML, STATE_FIELD, ERR, ERROR,)
	Returns the state field for the given CellML environment. More...

subroutine	cellml_state_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment models field. More...

subroutine	cellml_field_component_get_c (CELLML, MODEL_INDEX, CELLML_FIELD_TYPE, VARIABLE_ID, COMPONENT_USER_NUMBER, ERR, ERROR,)
	Find the component ID in the given field for the variable defined by the given variable ID in the provided CellML environment. This generic routine will be used to map variable ID's in CellML models to components in the various fields defined in the CellML models defined for the provided CellML environment. More...

subroutine	cellml_field_component_get_vs (CELLML, MODEL_INDEX, CELLML_FIELD_TYPE, VARIABLE_ID, COMPONENT_USER_NUMBER, ERR, ERROR,)
	Find the component ID in the given field for the variable defined by the given variable ID in the provided CellML environment. This generic routine will be used to map variable ID's in CellML models to components in the various fields defined in the CellML models defined for the provided CellML environment. More...

subroutine, public	cellml_intermediate_field_create_start (INTERMEDIATE_FIELD_USER_NUMBER, CELLML, INTERMEDIATE_FIELD, ERR, ERROR,)
	Create a field used to store intermediate variables of interest. More...

subroutine, public	cellml_intermediate_field_create_finish (CELLML, ERR, ERROR,)
	Finialse the creation of the intermediate field for the given CellML environment. Finish creating the intermediate variable field for the provided CellML environment. More...

subroutine	cellml_intermediate_field_finalise (INTERMEDIATE_FIELD, ERR, ERROR,)
	Finalise a CellML environment models field and deallocate all memory. More...

subroutine, public	cellml_intermediate_field_get (CELLML, INTERMEDIATE_FIELD, ERR, ERROR,)
	Returns the intermediate field for the given CellML environment. More...

subroutine	cellml_intermediate_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment intermediate field. More...

subroutine, public	cellml_parameters_field_create_start (PARAMETERS_FIELD_USER_NUMBER, CELLML, PARAMETERS_FIELD, ERR, ERROR,)
	Start the creation of the parameters field for the given CellML environment. More...

subroutine, public	cellml_parameters_field_create_finish (CELLML, ERR, ERROR,)
	Finish the creation of the parameters field for the given CellML environment. More...

subroutine	cellml_parameters_field_finalise (PARAMETERS_FIELD, ERR, ERROR,)
	Finalise a CellML environment parameters field and deallocate all memory. More...

subroutine, public	cellml_parameters_field_get (CELLML, PARAMETERS_FIELD, ERR, ERROR,)
	Returns the parameters field for the given CellML environment. More...

subroutine	cellml_parameters_field_initialise (CELLML, ERR, ERROR,)
	Initialise a CellML environment parameters field. More...

subroutine, public	cellml_generate (CELLML, ERR, ERROR,)
	Validate and instantiate the specified CellML environment. Users should call this routine once they have set up the CellML environment to allow the CellML environment to be validated and instantiated into computable code. More...

subroutine, public	cellml_user_number_find (USER_NUMBER, REGION, CELLML, ERR, ERROR,)
	Finds and returns in CELLML a pointer to the CellML environment identified by USER_NUMBER on a region. If no CellML environment with that USER_NUMBER exists CELLML is left nullified. More...

subroutine, public	cellml_environments_finalise (CELLML_ENVIRONMENTS, ERR, ERROR,)
	Finalises the CellML environments and deallocates all memory. More...

subroutine, public	cellml_environments_initialise (REGION, ERR, ERROR,)
	Initialises the CellML environments. More...

integer(intg) function	map_cellml_variable_type_to_field_type_intg (CELLML_VARIABLE_TYPE, ERR, ERROR)
	Maps a CellML variable type to a CellML field type (. More...

integer(intg) function	map_cellml_field_type_to_variable_type_intg (CELLML_FIELD_TYPE, ERR, ERROR)
	Maps a CellML field type to a CellML variable type (. More...

Variables
integer(intg), parameter, public	cellml_models_field = 1
	CellML models field. More...

integer(intg), parameter, public	cellml_state_field = 2
	CellML state field. More...

integer(intg), parameter, public	cellml_intermediate_field = 3
	CellML intermediate field. More...

integer(intg), parameter, public	cellml_parameters_field = 4
	CellML parameters field. More...

integer(intg), parameter	cellml_map_to_field_type = 1
	A CellML to field mapping type. More...

integer(intg), parameter	cellml_map_from_field_type = 2
	A field to CellML mapping type. More...

integer(intg), parameter	cellml_models_field_not_checked = -2
	The CellML environment models field has not been checked. More...

integer(intg), parameter, public	cellml_models_field_not_constant =-1
	The CellML environement models field is not constant. More...

Detailed Description

This module is a OpenCMISS(cm) buffer module to OpenCMISS(cellml).

Function/Subroutine Documentation

subroutine, public cmiss_cellml::cellml_cellml_to_field_update	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Updates any mapped fields from the cellml fields.

Parameters

	cellml	A pointer to the CellML environment to update
[out]	err	The error code
[out]	error	The error string

Definition at line 206 of file cmiss_cellml.f90.

References cellml_intermediate_field, cellml_models_field, cellml_models_field_not_constant, cellml_parameters_field, cellml_state_field, base_routines::diagnostic_output_type, base_routines::diagnostics1, base_routines::enters(), and base_routines::exits().

Referenced by solver_routines::solver_cellml_evaluator_solve(), solver_routines::solver_dae_bdf_solve(), solver_routines::solver_dae_euler_forward_solve(), and solver_routines::solver_dae_external_solve().

subroutine cmiss_cellml::cellml_create_cellml_to_field_map_c	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_INDEX,
		character(len=*), intent(in)	VARIABLE_ID,
		integer(intg), intent(in)	CELLML_PARAMETER_SET,
		type(field_type), intent(in), pointer	FIELD,
		integer(intg), intent(in)	VARIABLE_TYPE,
		integer(intg), intent(in)	COMPONENT_NUMBER,
		integer(intg), intent(in)	FIELD_PARAMETER_SET,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Create a CellML model variable to field variable component map.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	model_index	The index of the CellML model to map from.
[in]	variable_id	The ID of the CellML variable in the given model to map from.
[in]	cellml_parameter_set	The CellML parameter set to map from.
[in]	field	The field to map to.
[in]	variable_type	The field variable to map to.
[in]	component_number	The field variable component number to map to.
[in]	field_parameter_set	The field variable parameter set to map to.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 1998 of file cmiss_cellml.f90.

References cellml_map_from_field_type, cellml_model_map_initialise(), cmiss_fortran_c::cmissf2cstring(), base_routines::diagnostic_output_type, base_routines::diagnostics1, base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_create_cellml_to_field_map_vs	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_USER_NUMBER,
		type(varying_string), intent(in)	VARIABLE_ID,
		integer(intg), intent(in)	CELLML_PARAMETER_SET,
		type(field_type), intent(in), pointer	FIELD,
		integer(intg), intent(in)	VARIABLE_TYPE,
		integer(intg), intent(in)	COMPONENT_NUMBER,
		integer(intg), intent(in)	FIELD_PARAMETER_SET,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Create a CellML model variable to field variable component map.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	model_user_number	The user number of the CellML model to map from.
[in]	variable_id	The ID of the CellML variable in the given model to map from.
[in]	cellml_parameter_set	The CellML parameter set to map from.
[in]	field	The field to map to.
[in]	variable_type	The field variable to map to.
[in]	component_number	The field variable component number to map to.
[in]	field_parameter_set	The field variable parameter set to map to.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2205 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_create_field_to_cellml_map_c	(	type(cellml_type), pointer	CELLML,
		type(field_type), intent(in), pointer	FIELD,
		integer(intg), intent(in)	VARIABLE_TYPE,
		integer(intg), intent(in)	COMPONENT_NUMBER,
		integer(intg), intent(in)	FIELD_PARAMETER_SET,
		integer(intg), intent(in)	MODEL_INDEX,
		character(len=*), intent(in)	VARIABLE_ID,
		integer(intg), intent(in)	CELLML_PARAMETER_SET,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Create a field variable component to CellML model variable map.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	field	The field to map from.
[in]	variable_type	The field variable type to map from.
[in]	component_number	The field variable component number to map from.
[in]	field_parameter_set	The field variable parameter set to map from.
[in]	model_index	The index of the CellML model to map to.
[in]	variable_id	The ID of the CellML variable in the given model to map to.
[in]	cellml_parameter_set	The CellML parameter set to map to.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2245 of file cmiss_cellml.f90.

References cellml_map_to_field_type, cellml_model_map_initialise(), cmiss_fortran_c::cmissf2cstring(), base_routines::diagnostic_output_type, base_routines::diagnostics1, base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_create_field_to_cellml_map_vs	(	type(cellml_type), pointer	CELLML,
		type(field_type), intent(in), pointer	FIELD,
		integer(intg), intent(in)	VARIABLE_TYPE,
		integer(intg), intent(in)	COMPONENT_NUMBER,
		integer(intg), intent(in)	FIELD_PARAMETER_SET,
		integer(intg), intent(in)	MODEL_USER_NUMBER,
		type(varying_string), intent(in)	VARIABLE_ID,
		integer(intg), intent(in)	CELLML_PARAMETER_SET,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Create a field variable component to CellML model variable map.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	field	The field to map from.
[in]	variable_type	The field variable type to map from.
[in]	component_number	The field variable component number to map from.
[in]	field_parameter_set	The field variable parameter set to map from.
[in]	model_user_number	The user number of the CellML model to map to.
[in]	variable_id	The ID of the CellML variable in the given model to map to.
[in]	cellml_parameter_set	The CellML parameter set to map to.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2439 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_create_finish	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finish creating the CellML environment. At this point we know all the variables that are known and wanted so can generate the final code. Check the provided CellML environment object and if it all looks good clear the "in progress" flag to indicate the object is now ready for use.

Parameters

	cellml	The CellML environment object to check and finialise creation of.
[out]	err	The error code
[out]	error	The error string

Definition at line 655 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_create_start	(	integer(intg), intent(in)	CELLML_USER_NUMBER,
		type(region_type), intent(in), pointer	REGION,
		type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Set up the CellML environment in the given region. For a given region, create a CellML environment that will be used to define CellML models in openCMISS. This will simply create and initialise an empty CellML environment object in the specified region with the specified unique identifier number. Also set some flag to indicate the CellML environment object is in the process of being created and should not yet be used.

Todo:: Should be passing in a region? or leave that for the field mapping?

Parameters

[in]	cellml_user_number	The user specified ID for this CellML environment.
[in]	region	The region this CellML environment belongs to.
	cellml	The newly created CellML environment object.
[out]	err	The error code
[out]	error	The error string

Definition at line 575 of file cmiss_cellml.f90.

References cellml_initialise(), cellml_user_number_find(), base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_destroy	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Destroys the given CellML environment.

Parameters

	cellml	A pointer to the CellML environment to destroy
[out]	err	The error code
[out]	error	The error string

Definition at line 720 of file cmiss_cellml.f90.

References cellml_finalise(), base_routines::enters(), base_routines::exits(), and kinds::ptr.

subroutine, public cmiss_cellml::cellml_environments_finalise	(	type(cellml_environments_type), pointer	CELLML_ENVIRONMENTS,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finalises the CellML environments and deallocates all memory.

Parameters

	cellml_environments	A pointer to the CellML environments to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 4394 of file cmiss_cellml.f90.

References cellml_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_environments_initialise(), and region_routines::region_finalise().

subroutine, public cmiss_cellml::cellml_environments_initialise	(	type(region_type), pointer	REGION,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Initialises the CellML environments.

Parameters

	region	A pointer to the region to initialise the CellML environments for
[out]	err	The error code
[out]	error	The error string

Definition at line 4426 of file cmiss_cellml.f90.

References cellml_environments_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by region_routines::region_initialise().

subroutine cmiss_cellml::cellml_field_component_get_c	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_INDEX,
		integer(intg), intent(in)	CELLML_FIELD_TYPE,
		character(len=*), intent(in)	VARIABLE_ID,
		integer(intg), intent(out)	COMPONENT_USER_NUMBER,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Find the component ID in the given field for the variable defined by the given variable ID in the provided CellML environment. This generic routine will be used to map variable ID's in CellML models to components in the various fields defined in the CellML models defined for the provided CellML environment.

may need to also provide a FIELD_VARIABLE_NUMBER (always 1?) for completeness
is the model ID also needed?
because the CellML fields should all be set up to allow direct use in the CellML code, the component number matches the index of the given variable in its associated array in the CellML generated code.

Parameters

	cellml	The CellML environment object from which to get the field component.
[in]	model_index	The index of the CellML model to map from.
[in]	cellml_field_type	The type of CellML field type to get the component for.

See also: CMISS_CELLML::FieldTypes,CMISS_CELLML

Parameters

[in]	variable_id	The ID of the model variable which needs to be located in the provided field.
[out]	component_user_number	On return, the field component for the model variable defined by the given ID.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3423 of file cmiss_cellml.f90.

References cmiss_fortran_c::cmissf2cstring(), base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_field_component_get_vs	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_INDEX,
		integer(intg), intent(in)	CELLML_FIELD_TYPE,
		type(varying_string), intent(in)	VARIABLE_ID,
		integer(intg), intent(out)	COMPONENT_USER_NUMBER,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Find the component ID in the given field for the variable defined by the given variable ID in the provided CellML environment. This generic routine will be used to map variable ID's in CellML models to components in the various fields defined in the CellML models defined for the provided CellML environment.

may need to also provide a FIELD_VARIABLE_NUMBER (always 1?) for completeness
is the model ID also needed?

Parameters

	cellml	The CellML environment object from which to get the field component.
[in]	model_index	The index of the CellML model to map from.
[in]	cellml_field_type	The type of CellML field type to get the component for.

See also: CMISS_CELLML::FieldTypes,CMISS_CELLML

Parameters

[in]	variable_id	The ID of the model variable which needs to be located in the provided field.
[out]	component_user_number	On return, the field component for the model variable defined by the given ID.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3479 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_field_maps_create_finish	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finish creating the field maps for a CellML environment.

Parameters

	cellml	The CellML environment to finish creating the maps for.
[out]	err	The error code
[out]	error	The error string

Definition at line 1248 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_field_maps_create_start	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Start the creation of field maps for a CellML environment.

Parameters

	cellml	The CellML environment to create the maps for.
[out]	err	The error code
[out]	error	The error string

Definition at line 1313 of file cmiss_cellml.f90.

References cellml_field_maps_initialise(), base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_field_maps_finalise	(	type(cellml_field_maps_type), pointer	CELLML_FIELD_MAPS,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML maps and deallocate all memory.

Parameters

	cellml_field_maps	A pointer to the CellML field maps to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 1353 of file cmiss_cellml.f90.

References cellml_model_maps_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_field_maps_initialise(), and cellml_finalise().

subroutine cmiss_cellml::cellml_field_maps_initialise	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML field mpas.

Parameters

	cellml	A pointer to the CellML environment to initialise the field maps for
[out]	err	The error code
[out]	error	The error string

Definition at line 1392 of file cmiss_cellml.f90.

References cellml_field_maps_finalise(), cellml_model_maps_initialise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_field_maps_create_start().

subroutine, public cmiss_cellml::cellml_field_to_cellml_update	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Updates any cellml fields from the mapped fields.

Parameters

	cellml	A pointer to the CellML environment to update
[out]	err	The error code
[out]	error	The error string

Definition at line 785 of file cmiss_cellml.f90.

References cellml_intermediate_field, cellml_models_field, cellml_models_field_not_constant, cellml_parameters_field, cellml_state_field, base_routines::diagnostic_output_type, base_routines::diagnostics1, base_routines::enters(), and base_routines::exits().

Referenced by solver_routines::solver_cellml_evaluator_solve(), solver_routines::solver_dae_bdf_solve(), solver_routines::solver_dae_euler_forward_solve(), and solver_routines::solver_dae_external_solve().

subroutine, public cmiss_cellml::cellml_fieldmodeldofset	(	type(field_variable_type), pointer	modelVariable,
		integer(intg), intent(in)	modelDofIdx,
		type(field_type), pointer	field,
		integer(intg), intent(in)	variableType,
		integer(intg), intent(in)	parameterSetIdx,
		integer(intg), intent(in)	componentIdx,
		real(dp), intent(in)	value,
		integer(intg), intent(out)	err,
		type(varying_string), intent(out)	error
	)

Set the dof in a field specified by a model DOF and component to a value.

Parameters

	modelvariable	A pointer to the model field variable
[in]	modeldofidx	The model dof to set.
	field	A pointer to the field to set the value for
[in]	variabletype	The variable type to set the value for
[in]	parametersetidx	The parameter set index of the field variable to set.
[in]	componentidx	The component index of the field variable to set.
[in]	value	The value to set.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2479 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_parameters_field_create_finish(), and cellml_state_field_create_finish().

subroutine cmiss_cellml::cellml_finalise	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML environment and deallocate all memory.

Parameters

	cellml	A pointer to the CellML environment to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 1151 of file cmiss_cellml.f90.

References cellml_field_maps_finalise(), cellml_intermediate_field_finalise(), cellml_model_finalise(), cellml_models_field_finalise(), cellml_parameters_field_finalise(), cellml_state_field_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_destroy(), cellml_environments_finalise(), and cellml_initialise().

subroutine, public cmiss_cellml::cellml_generate	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Validate and instantiate the specified CellML environment. Users should call this routine once they have set up the CellML environment to allow the CellML environment to be validated and instantiated into computable code.

generate and compile code.
distribute things amonst processors?
create the internal fields?
does this method need to get called or can it be done implicitly as needed by other solution procedures?

Parameters

	cellml	The CellML environment object for which to generate computable code.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 4299 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_initialise	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML environment and deallocate all memory.

Parameters

	cellml	A pointer to the CellML environment to initialise.
[out]	err	The error code
[out]	error	The error string

Definition at line 1195 of file cmiss_cellml.f90.

References cellml_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_create_start().

subroutine, public cmiss_cellml::cellml_intermediate_field_create_finish	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finialse the creation of the intermediate field for the given CellML environment. Finish creating the intermediate variable field for the provided CellML environment.

check for valid variables being defined?
maybe delete the field if no valid variables/components exist?

Parameters

	cellml	The CellML environment object for which to finalise the creation of the intermediate field.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3684 of file cmiss_cellml.f90.

References cellml_models_field_check(), base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_intermediate_field_create_start	(	integer(intg), intent(in)	INTERMEDIATE_FIELD_USER_NUMBER,
		type(cellml_type), pointer	CELLML,
		type(field_type), pointer	INTERMEDIATE_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Create a field used to store intermediate variables of interest.

Parameters

[in]	intermediate_field_user_number	The unique identifier for the intermediate field to be created for the given CellML environment object.
	cellml	The CellML environment object from which to get the field component.
	intermediate_field	If associated on entry, a pointer to the user created intermediate field which has the same user number as the specified intermediate field user number. If not associated on entry, on exit, a pointer to the created intermediate field for the CellML environment.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3513 of file cmiss_cellml.f90.

References cellml_intermediate_field_initialise(), base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_intermediate_field_finalise	(	type(cellml_intermediate_field_type), pointer	INTERMEDIATE_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML environment models field and deallocate all memory.

Parameters

	intermediate_field	A pointer to the CellML environment intermediate field to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 3741 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_finalise(), and cellml_intermediate_field_initialise().

subroutine, public cmiss_cellml::cellml_intermediate_field_get	(	type(cellml_type), pointer	CELLML,
		type(field_type), pointer	INTERMEDIATE_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Returns the intermediate field for the given CellML environment.

Parameters

	cellml	The CellML environment object from which to get the intermediate field.
	intermediate_field	On return, a pointer to the intermediate field for this CellML environment.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3773 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_intermediate_field_initialise	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML environment intermediate field.

Parameters

	cellml	A pointer to the CellML environment to initialise the intermediate field for.
[out]	err	The error code
[out]	error	The error string

Definition at line 3821 of file cmiss_cellml.f90.

References cellml_intermediate_field_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_intermediate_field_create_start().

subroutine cmiss_cellml::cellml_model_finalise	(	type(cellml_model_type), pointer	CELLML_MODEL,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML model and deallocate all memory.

Parameters

	cellml_model	A pointer to the CellML model to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 1454 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_finalise(), and cellml_model_initialise().

subroutine cmiss_cellml::cellml_model_import_c	(	type(cellml_type), pointer	CELLML,
		character(len=*)	URI,
		integer(intg), intent(out)	MODEL_INDEX,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Import the specified CellML model into the given CellML environment object.

Parameters

	cellml	The CellML environment object into which we want to import the specified model.
	uri	The (absolute? relative?) URI of the model to import. As per tracker item 2013 comment 8 the URI should now simply point to a CellML document. Can use a relative URL which will be interpreted relative to the CWD of the executed application.
[out]	model_index	On return, the index for this model within the given CellML environment object.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 1701 of file cmiss_cellml.f90.

References cellml_model_initialise(), base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_model_import_vs	(	type(cellml_type), pointer	CELLML,
		type(varying_string), intent(in)	URI,
		integer(intg), intent(out)	MODEL_INDEX,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Import the specified CellML model into the given CellML environment object.

Parameters

	cellml	The CellML environment object into which we want to import the specified model.
[in]	uri	The (absolute? relative?) URI of the model to import. As per tracker item 2013 comment 8 the URI should now simply point to a CellML document. Can use a relative URL which will be interpreted relative to the CWD of the executed application.
[out]	model_index	On return, the index for this model within the given CellML environment object.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 1769 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_model_initialise	(	type(cellml_model_type), pointer	CELLML_MODEL,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML model.

Parameters

	cellml_model	On return, a pointer to the CellML initialised model. Must not be associated on entry.
[out]	err	The error code
[out]	error	The error string

Definition at line 1488 of file cmiss_cellml.f90.

References cellml_model_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_model_import_c().

subroutine cmiss_cellml::cellml_model_map_finalise	(	type(cellml_model_map_type), pointer	CELLML_MODEL_MAP,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML model map and deallocate all memory.

Parameters

	cellml_model_map	A pointer to the CellML model map to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 1534 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_model_map_initialise(), and cellml_model_maps_finalise().

subroutine cmiss_cellml::cellml_model_map_initialise	(	type(cellml_model_map_type), pointer	CELLML_MODEL_MAP,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML model map.

Parameters

	cellml_model_map	On return, a pointer to the CellML initialised model map field. Must not be associated on entry.
[out]	err	The error code
[out]	error	The error string

Definition at line 1567 of file cmiss_cellml.f90.

References cellml_model_map_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_create_cellml_to_field_map_c(), and cellml_create_field_to_cellml_map_c().

subroutine cmiss_cellml::cellml_model_maps_finalise	(	type(cellml_model_maps_type), pointer	CELLML_MODEL_MAPS,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML model maps and deallocate all memory.

Parameters

	cellml_model_maps	A pointer to the CellML model maps to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 1615 of file cmiss_cellml.f90.

References cellml_model_map_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_field_maps_finalise(), and cellml_model_maps_initialise().

subroutine cmiss_cellml::cellml_model_maps_initialise	(	type(cellml_model_maps_type), pointer	CELLML_MODEL_MAPS,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML model maps.

Parameters

	cellml_model_maps	On return, a pointer to the CellML initialised model maps. Must not be associated on entry.
[out]	err	The error code
[out]	error	The error string

Definition at line 1660 of file cmiss_cellml.f90.

References cellml_model_maps_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_field_maps_initialise().

subroutine cmiss_cellml::cellml_models_field_check	(	type(cellml_models_field_type), pointer	MODELS_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Checks a CellML environment models field for correctness.

Parameters

	models_field	A pointer to the CellML environment models field to check.
[out]	err	The error code
[out]	error	The error string

Definition at line 2557 of file cmiss_cellml.f90.

References cellml_models_field_not_checked, cellml_models_field_not_constant, base_routines::enters(), and base_routines::exits().

Referenced by cellml_intermediate_field_create_finish(), cellml_parameters_field_create_finish(), and cellml_state_field_create_finish().

subroutine, public cmiss_cellml::cellml_models_field_create_finish	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finish the creation of the models field for the given CellML environment.

Parameters

	cellml	The CellML environment object for which we need to finish creation of the models field.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2821 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_models_field_create_start	(	integer(intg), intent(in)	MODEL_FIELD_USER_NUMBER,
		type(cellml_type), pointer	CELLML,
		type(field_type), pointer	MODELS_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Start the creation of the models field for the given CellML environment.

Parameters

[in]	model_field_user_number	The unique identifier for the models field to be created for the given CellML environment object.
	cellml	The CellML environment object for which we need to create the models field.
	models_field	If associated on entry, a pointer to the user created models field which has the same user number as the specified models field user number. If not associated on entry, on exit, a pointer to the created models field for the CellML environment.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2662 of file cmiss_cellml.f90.

References cellml_models_field_initialise(), base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_models_field_finalise	(	type(cellml_models_field_type), pointer	MODELS_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML environment models field and deallocate all memory.

Parameters

	models_field	A pointer to the CellML environment models field to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 2871 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_finalise(), and cellml_models_field_initialise().

subroutine, public cmiss_cellml::cellml_models_field_get	(	type(cellml_type), pointer	CELLML,
		type(field_type), pointer	MODELS_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Returns the models field for the given CellML environment.

Parameters

	cellml	The CellML environment object from which to get the models field.
	models_field	On return, a pointer to the models field for this CellML environment. Must not be associated on entry.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2903 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_models_field_initialise	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML environment models field.

Parameters

	cellml	A pointer to the CellML environment to initialise the models field for.
[out]	err	The error code
[out]	error	The error string

Definition at line 2951 of file cmiss_cellml.f90.

References cellml_models_field_finalise(), cellml_models_field_not_checked, base_routines::enters(), and base_routines::exits().

Referenced by cellml_models_field_create_start().

subroutine, public cmiss_cellml::cellml_parameters_field_create_finish	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finish the creation of the parameters field for the given CellML environment.

Parameters

	cellml	The CellML environment object for which to finalise the parameters field.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 4034 of file cmiss_cellml.f90.

References cellml_fieldmodeldofset(), cellml_models_field_check(), cellml_models_field_not_constant, cellml_parameters_field, base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_parameters_field_create_start	(	integer(intg), intent(in)	PARAMETERS_FIELD_USER_NUMBER,
		type(cellml_type), pointer	CELLML,
		type(field_type), pointer	PARAMETERS_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Start the creation of the parameters field for the given CellML environment.

Parameters

[in]	parameters_field_user_number	The unique identifier for the parameters field to be created for the given CellML environment object.
	cellml	The CellML environment object for which we will be defining the parameters field.
	parameters_field	If associated on entry, a pointer to the user created parameters field which has the same user number as the specified parameters field user number. If not associated on entry, on exit, a pointer to the created parameters field for the CellML environment.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3867 of file cmiss_cellml.f90.

References cellml_parameters_field_initialise(), base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_parameters_field_finalise	(	type(cellml_parameters_field_type), pointer	PARAMETERS_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML environment parameters field and deallocate all memory.

Parameters

	parameters_field	A pointer to the CellML environment parameters field to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 4169 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_finalise(), and cellml_parameters_field_initialise().

subroutine, public cmiss_cellml::cellml_parameters_field_get	(	type(cellml_type), pointer	CELLML,
		type(field_type), pointer	PARAMETERS_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Returns the parameters field for the given CellML environment.

Parameters

	cellml	The CellML environment object from which to get the parameters field.
	parameters_field	On return, a pointer to the parameters field for this CellML environment. Must not be associated on entry.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 4201 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_parameters_field_initialise	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML environment parameters field.

Parameters

	cellml	A pointer to the CellML environment to initialise the models field for.
[out]	err	The error code
[out]	error	The error string

Definition at line 4248 of file cmiss_cellml.f90.

References cellml_parameters_field_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_parameters_field_create_start().

subroutine, public cmiss_cellml::cellml_state_field_create_finish	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finialse the creation of the state field for the given CellML environment. Finish creating the state variable field for the provided CellML environment.

default field values are set for all components in the field at all DOFs based on the initial_value's from the CellML model

Parameters

	cellml	The CellML environment object for which to finalise the creation of the state field.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3164 of file cmiss_cellml.f90.

References cellml_fieldmodeldofset(), cellml_models_field_check(), cellml_models_field_not_constant, cellml_state_field, base_routines::enters(), and base_routines::exits().

subroutine, public cmiss_cellml::cellml_state_field_create_start	(	integer(intg), intent(in)	STATE_FIELD_USER_NUMBER,
		type(cellml_type), pointer	CELLML,
		type(field_type), pointer	STATE_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Start the creation of the state field for the given CellML environment.

Parameters

[in]	state_field_user_number	The unique identifier for the state field to be created for the given CellML environment object.
	cellml	The CellML environment object for which to create the state field.
	state_field	If associated on entry, a pointer to the user created state field which has the same user number as the specified state field user number. If not associated on entry, on exit, a pointer to the created state field for the CellML environment.
[out]	err	The error code.
[out]	error	The error string.

Definition at line 2998 of file cmiss_cellml.f90.

References cellml_state_field_initialise(), base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_state_field_finalise	(	type(cellml_state_field_type), pointer	STATE_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Finalise a CellML environment state field and deallocate all memory.

Parameters

	state_field	A pointer to the CellML environment state field to finalise.
[out]	err	The error code
[out]	error	The error string

Definition at line 3293 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_finalise(), and cellml_state_field_initialise().

subroutine, public cmiss_cellml::cellml_state_field_get	(	type(cellml_type), pointer	CELLML,
		type(field_type), pointer	STATE_FIELD,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Returns the state field for the given CellML environment.

Parameters

	cellml	The CellML environment object from which to get the state field.
	state_field	On successful return will be set to the state field for this CellML environment
[out]	err	The error code.
[out]	error	The error string.

Definition at line 3325 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_state_field_initialise	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Initialise a CellML environment models field.

Parameters

	cellml	A pointer to the CellML environment to initialise the models field for.
[out]	err	The error code
[out]	error	The error string

Definition at line 3373 of file cmiss_cellml.f90.

References cellml_state_field_finalise(), base_routines::enters(), and base_routines::exits().

Referenced by cellml_state_field_create_start().

subroutine, public cmiss_cellml::cellml_user_number_find	(	integer(intg), intent(in)	USER_NUMBER,
		type(region_type), pointer	REGION,
		type(cellml_type), pointer	CELLML,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

Finds and returns in CELLML a pointer to the CellML environment identified by USER_NUMBER on a region. If no CellML environment with that USER_NUMBER exists CELLML is left nullified.

Parameters

[in]	user_number	The user number to find.
	region	A pointer to the region to find the CellML user number.
	cellml	On return a pointer to the CellML environment with the given user number. If no CellML environment with that user number exists then the pointer is returned as NULL. Must not be associated on entry.
[out]	err	The error code
[out]	error	The error string

Definition at line 4338 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

Referenced by cellml_create_start().

subroutine cmiss_cellml::cellml_variable_set_as_known_c	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_INDEX,
		character(len=*), intent(in)	VARIABLE_ID,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Sets a CellML model variable to be known - i.e., the variable's value will be set by an OpenCMISS field.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	model_index	The index of the CellML model in which to find the given variable.
[in]	variable_id	The CellML variable to set as known (in the format 'component_name/variable_name').
[out]	err	The error code.
[out]	error	The error string.

Definition at line 1801 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_variable_set_as_known_vs	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_USER_NUMBER,
		type(varying_string), intent(in)	VARIABLE_ID,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Sets a CellML model variable to be known - i.e., the variable's value will be set by an OpenCMISS field.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	model_user_number	The index of the CellML model in which to find the given variable.
[in]	variable_id	The CellML variable to set as known (in the format 'component_name/variable_name').
[out]	err	The error code.
[out]	error	The error string.

Definition at line 1866 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_variable_set_as_wanted_c	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_INDEX,
		character(len=*), intent(in)	VARIABLE_ID,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Sets a CellML model variable to be wanted - i.e., the variable's value will used by an OpenCMISS field.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	model_index	The index of the CellML model in which to find the given variable.
[in]	variable_id	The CellML variable to set as wanted (in the format 'component_name/variable_name').
[out]	err	The error code.
[out]	error	The error string.

Definition at line 1899 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

subroutine cmiss_cellml::cellml_variable_set_as_wanted_vs	(	type(cellml_type), pointer	CELLML,
		integer(intg), intent(in)	MODEL_USER_NUMBER,
		type(varying_string), intent(in)	VARIABLE_ID,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Sets a CellML model variable to be wanted - i.e., the variable's value will be used by an OpenCMISS field.

Parameters

	cellml	The CellML environment object in which to create the map.
[in]	model_user_number	The index of the CellML model in which to find the given variable.
[in]	variable_id	The CellML variable to set as wanted (in the format 'component_name/variable_name').
[out]	err	The error code.
[out]	error	The error string.

Definition at line 1964 of file cmiss_cellml.f90.

References base_routines::enters(), and base_routines::exits().

integer(intg) function cmiss_cellml::map_cellml_field_type_to_variable_type_intg	(	integer(intg), intent(in)	CELLML_FIELD_TYPE,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Maps a CellML field type to a CellML variable type (.

See also: CMISS_CELLML::FieldTypes,CMISS_CELLML)

Parameters

[in]	cellml_field_type	The CellML field type to map.
[out]	err	The error code
[out]	error	The error string

Definition at line 4508 of file cmiss_cellml.f90.

References cellml_intermediate_field, cellml_parameters_field, cellml_state_field, base_routines::enters(), and base_routines::exits().

integer(intg) function cmiss_cellml::map_cellml_variable_type_to_field_type_intg	(	integer(intg), intent(in)	CELLML_VARIABLE_TYPE,
		integer(intg), intent(out)	ERR,
		type(varying_string), intent(out)	ERROR
	)

private

Maps a CellML variable type to a CellML field type (.

See also: CMISS_CELLML::FieldTypes,CMISS_CELLML)

Parameters

[in]	cellml_variable_type	The CellML variable type to map.
[out]	err	The error code
[out]	error	The error string

Definition at line 4463 of file cmiss_cellml.f90.

References cellml_intermediate_field, cellml_parameters_field, cellml_state_field, base_routines::enters(), and base_routines::exits().

Data Types

Functions/Subroutines

Variables

Detailed Description

Function/Subroutine Documentation